Examples

This section is a compact template library. Pick one example and run it directly.

Recommended Order

1. Basic Molecules

2. Machine Learning Examples

3. Mode3 Top-20 Remote Debug (Linux, No SLURM)

Use Case Map

• Learn the full pipeline quickly: Basic Molecules

• Focus on modeling and SHAP: Machine Learning Examples

• Reproduce remote Linux debugging workflow: Mode3 Top-20 Remote Debug (Linux, No SLURM)

• Need larger systems: Complex Systems

• Need custom orchestration: Custom Workflows

Fast Start Commands

# Full workflow
surfacia workflow -i molecules.csv --test-samples "1,3"

# ML only
surfacia ml-analysis -i FinalFull_Mode3_20_168.csv --test-samples "1,2,3"

# Visualization
surfacia shap-viz -i Training_Set_Detailed.csv -x ./xyz_files/

Example Pages

• Basic Molecules
  • Good Starting Systems
  • Suggested Mini Set
  • Example Input Table
  • Suggested Command Sequence
  • What to Compare First
  • What These Examples Are Good For
  • What You Can Usually Observe
  • How to Read the Results
  • Simple Interpretation Template
  • What Counts as a Healthy Output
  • Why This Example Matters
• Complex Systems
  • Representative Use Cases
  • Representative Surfacia Scenarios
  • How to Decide Which Mode to Try
  • Suggested Working Sequence
  • Result Interpretation Template
  • How to Approach Them
  • Why They Matter
  • Typical Payoff
  • What to Watch For
  • What Often Works Well
• Machine Learning Examples
  • Typical Questions
  • Example Patterns Worth Studying
  • Suggested Minimal Pipeline
  • What to Compare
  • Practical Reading Strategy
  • Useful Comparison Table
  • Result Review Template
  • What to Do When the Score Is Good but the Story Is Weak
• Custom Workflows
  • Examples
  • Useful Real-World Patterns
  • Pattern 1: Reuse Descriptors
  • Pattern 2: Compare Modes on the Same Problem
  • Pattern 3: Interpretation-First Projects
  • Pattern 4: Long-Running Resume Workflows
  • Why This Matters
  • Recommended Mindset
  • Decision Checklist
• Mode3 Top-20 Remote Debug (Linux, No SLURM)
  • Goal
  • Run Context
  • Environment Setup
  • Step-7 Command (Validated)
  • Observed Errors and Fixes
  • Results Checklist